Summary

1. The stable carbon isotope ratio δ13C is a useful tracer of energy flow in lake food webs, and the zooplankton signature is commonly used to establish a baseline for the pelagic habitat. However, sources of temporal variability in the δ13C of different zooplankton taxa are rarely considered.

2. Here, we investigate to what extent temporal variation in the δ13C of particulate organic matter (POM) (<41 μm) and the C : N of zooplankton can explain the temporal variability in δ13C of freshwater zooplankton. We compare temporal patterns of δ13C and C : N for Daphnia, Hesperodiaptomus franciscanus and Leptodiaptomus tyrelli over a 6-month period at four sites in two oligotrophic lakes.

3. In all three taxa, seasonal variation in zooplankton C : N explained more of the variation in zooplankton δ13C than did the δ13C of POM. This suggests that variation in the lipid content of zooplankton can strongly influence temporal variation of δ13C in zooplankton.

4. Using these data, we evaluate procedures that estimate the δ13C of only the non-lipid component of zooplankton. If zooplankton lipids are primarily dietary in origin, than extracting lipids or ‘normalising’δ13C based on C : N will exclude a major dietary source, and therefore may be inappropriate.